nf-metro¶

Generate metro-map-style SVG diagrams from Mermaid graph definitions with %%metro directives. Designed for visualizing bioinformatics pipeline workflows (e.g., nf-core pipelines) as transit-style maps where each analysis route is a colored "metro line."

nf-core/rnaseq metro map

Installation¶

pip (PyPI)¶

pip install nf-metro

Conda (Bioconda)¶

conda install bioconda::nf-metro

Container (Seqera Containers)¶

A pre-built container is available via Seqera Containers:

docker pull community.wave.seqera.io/library/pip_nf-metro:611b1ba39c6007f1

Requires Python 3.10+.

Quick start¶

Render a metro map from a .mmd file:

nf-metro render examples/simple_pipeline.mmd -o pipeline.svg

Validate your input without rendering:

nf-metro validate examples/simple_pipeline.mmd

Inspect structure (sections, lines, stations):

nf-metro info examples/simple_pipeline.mmd

CLI reference¶

`nf-metro render`¶

Render a Mermaid metro map definition to SVG.

nf-metro render [OPTIONS] INPUT_FILE

Option	Default	Description
`-o`, `--output PATH`	`<input>.svg`	Output SVG file path
`--theme [nfcore\\|light]`	`nfcore`	Visual theme
`--width INTEGER`	auto	SVG width in pixels
`--height INTEGER`	auto	SVG height in pixels
`--x-spacing FLOAT`	`60`	Horizontal spacing between layers
`--y-spacing FLOAT`	`40`	Vertical spacing between tracks
`--max-layers-per-row INTEGER`	auto	Max layers before folding to next row
`--animate / --no-animate`	off	Add animated balls traveling along lines
`--debug / --no-debug`	off	Show debug overlay
`--logo PATH`	none	Logo image path (overrides `%%metro logo:` directive)
`--from-nextflow`	off	Convert Nextflow `-with-dag` input before rendering
`--title TEXT`	none	Pipeline title (used with `--from-nextflow`)

`nf-metro convert`¶

Convert a Nextflow -with-dag mermaid file to nf-metro format.

nf-metro convert [OPTIONS] INPUT_FILE

Option	Default	Description
`-o`, `--output PATH`	stdout	Output `.mmd` file path
`--title TEXT`	auto	Pipeline title

See Importing from Nextflow for details and examples.

`nf-metro validate`¶

Check a .mmd file for errors without producing output.

nf-metro validate INPUT_FILE

`nf-metro info`¶

Print a summary of the parsed map: sections, lines, stations, and edges.

nf-metro info INPUT_FILE

Writing metro maps¶

Read the Guide to learn how to write .mmd files, from minimal examples to multi-section pipelines with custom grid layouts.

Gallery¶

See the Gallery for rendered examples covering simple pipelines, complex multi-line topologies, fan-out/fan-in patterns, fold layouts, and realistic bioinformatics workflows.

License¶

MIT